ToolUniverse is a collection of tools, interfaces, and supporting components for building AI systems that perform scientific work. It is for developers creating AI scientist agents that use APIs, databases, machine-learning tools, and domain-specific utilities. The catalogue includes skills, commands, an MCP server, an agent, and a hook for working with the ecosystem.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add mims-harvard/ToolUniverse --skill tooluniverse-ecology-biodiversitygit clone --depth 1 https://github.com/mims-harvard/ToolUniverseWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-ecology-biodiversity)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-ecology-biodiversity"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-ecology-biodiversity/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-ecology-biodiversity"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-ecology-biodiversity.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00070 | $0.01760 |
| Opus 5 | $0.00035 | $0.00880 |
| Sonnet 5 | $0.00014 | $0.00352 |
| Haiku 4.5 | $0.00007 | $0.00176 |
Grade A, and why
tooluniverse-ecology-biodiversity scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 13d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 102 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Ecology & Biodiversity Research
Reasoning Strategy
1. Species & Taxonomy Questions
When a question involves identifying or comparing species:
- LOOK UP DON'T GUESS — Use
GBIF_search_speciesto get taxonomy,WoRMS_search_speciesfor marine organisms - If the question asks about invasive species impacts, consider: ecological niche overlap, reproductive rate, predator release, and ecosystem engineering effects
- Use
PubMed_search_articlesorEuropePMC_search_articlesto find studies on specific ecological impacts
2. Invasive Species Impact Assessment
Reasoning framework — when comparing invasive species impacts:
- Identify the ecosystem: What habitat/biome is affected?
- Assess impact mechanisms: Competition? Predation? Disease vector? Habitat modification? Hybridization?
- Scale of impact: Local (single site) vs regional vs continental?
- Trophic position: Invasives at higher trophic levels (predators) often cause more damage than lower (herbivores)
- Ecosystem engineering: Species that modify habitats (beavers, earthworms, honeybees displacing native pollinators) cause outsized impacts
- Look up specifics — don't rely on general knowledge. Search for "[species name] invasive impact [region]" in literature
3. Pollinator Ecology
Reasoning framework for pollination questions:
- Foraging behavior: Distinguish investigation (approach/assessment) from actual feeding (proboscis insertion)
- Interaction types: Mutualistic (pollination reward), parasitic (nectar robbing), commensal
- Observation methods: Camera traps have resolution/FOV limitations — consider what's identifiable at given resolution
- Statistical considerations: Observer agreement (inter-rater reliability), sampling effort, temporal patterns
- Ethogram interpretation: Each behavior category has specific start/end criteria — follow them precisely
4. Population Dynamics
Reasoning framework for population ecology questions:
- Growth models: Exponential (unlimited), logistic (K-limited), Allee effects (low-density problems)
- Extinction analysis: Distinguish deterministic extinction (r < 0) from stochastic extinction (small population fluctuations)
- Survival analysis: Time-to-event analysis needs appropriate statistical tests (log-rank, Cox regression, Kaplan-Meier)
- Microbial ecology: For microbial stressor responses, use survival curve analysis with time-kill kinetics. To compare extinction points between populations, you need time-to-extinction data analyzed with survival statistics (not just endpoint comparisons)
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 13d ago First seen · 102 lines · 70 tokens per session scan A e57d13d74fe2
tooluniverse-ecology-biodiversity is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,680 stars, last pushed 3d ago), licensed Apache-2.0. It adds 70 tokens to every session and 1,760 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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